A thorough understanding of the phase behaviour of biomaterial composites is imperative for manipulating the structural and textural properties in novel food products. This study probed the phase behaviour of a model system comprising agarose and a varying concentration of ghee. Results obtained from scanning electron microscopy (SEM), micro differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR) and dynamic oscillation in-shear revealed discontinuous and hard inclusions of ghee reinforcing the continuous, weaker agarose matrix with increasing concentrations of the former. Phase behaviour of the system was quantified in parallel with a novel method combining 3D confocal laser scanning microscopy (CLSM) imaging and image analysis software - FIJI and Imaris - in an effort to substantiate the efficacy of the microscopic protocol in quantifying phase behaviour. Phase volumes recorded with the microscopic protocol were in close agreement to those modelled with the Lewis-Nielsen blending law using small-deformation dynamic oscillation. However, results indicated that the inner filtering effect or ‘self-shadowing’ observed commonly in CLSM images may pose a limitation to the application of this technique, necessitating further development before it can be applied to more complex, industrially relevant systems.